Molecule entity overview

  • Updated

Molecule entities enable your team to model, track, and visualize small molecules in Benchling. Use them in the Registry to model chemical compounds, then search for and visualize your molecules using our chemical structure-based search capabilities.

Molecule entity capabilities

Molecule entities enable you to create and model chemical compounds captured as chemical entities. With molecule entities, you can:

  • View calculated physicochemical properties

  • Find molecules via similarity and substructure search

  • Visualize chemical structures

You can create molecules in the Registry by:

  • Bulk importing via API, .sdf, or .csv

  • Registration tables using SMILES strings

  • Drawing chemicals using the Marvin JS chemical sketcher

You can use substructure and similarity searches to find molecules in the Registry.

Molecule entity limitations

At this time, molecule entities don’t support:

  • Molecules containing atom group notation, like R-groups, atom lists, atom NOT lists, any atoms, etc.

  • Chemical structures larger than 999 atoms

  • Molecules containing repeat notation (brackets and multiplier), typically found in large polymer structures

  • Organometallic compounds, inorganic compounds, or other structures that have more than one structural component

Enabling molecule entities

To enable molecule entities for your organization, contact your CX representative and account manager.

Was this article helpful?

Have more questions? Submit a request